def test_primer_design_overorigin(self):
"""Tests whether primers can be designed over an origin of a cyclic
sequence."""
fixtures = join(abspath(dirname(__file__)), "fixtures")
with open(join(fixtures, "template.txt")) as f:
template = f.read().strip()
region = Region(2020, 1616, len(template), cyclic=True)
adjusted_template = region.get_slice(template) + region.invert()[0].get_slice(
template
)
rprimer = "CGCTGGAGAAAACCTTCGTATCGGCgcatgcacgcgtgtcgacatcg"
assert (
rc("CGCTGGAGAAAACCTTCGTATCGGCgcatgcacgcgtgtcgacatcg".upper())
in adjusted_template.upper()
)
fwd, rev = anneal(adjusted_template, [rprimer])
print(rev[0]["top_strand_slice"])
rprimer = "CGCTGGAGAAAACCTTCGTATCGGCgcatgcacgcgtgtcgacatcg"
pairs, explain = _design_primers(template, region, None, rseq=rprimer)
print(json.dumps(pairs, indent=1))
print(explain)
assert pairs
def test_anneal():
s = "ACGTGTATGTGATGATGTGCGTGTGTCGTGTAGCTTATTATATGCGGAGTCGTTGATGCTGTGAGT"
fwd, rev = anneal(s, ["AAAAAGTGCGTGTGTCGTGTAG".lower()])
match = list(fwd)[0]
assert match["start"] == 16
assert match["start"] + match["length"] == 33
assert match["anneal"] == "GTGCGTGTGTCGTGTAG".lower()
assert match["overhang"] == "AAAAA".lower()
print(match)
def test_anneal_rev():
s = "ACGTGTATGTGATGATGTGCGTGTGTCGTGTAGCTTATTATATGCGGAGTCGTTGATGCTGTGAGT"
fwd, rev = list(anneal(s, ["ANNNN" + reverse_complement(s[20:40])]))
print(rev[0])
assert rev[0]["start"] == 39
assert rev[0]["top_strand_slice"] == (20, 40)
assert rev[0]["anneal"] == reverse_complement(s[20:40])
assert rev[0]["overhang"] == "ANNNN"
assert rev[0]["strand"] == -1
def test_anneal_fwd():
s = "ACGTGTATGTGATGATGTGCGTGTGTCGTGTAGCTTATTATATGCGGAGTCGTTGATGCTGTGAGT"
fwd, rev = list(anneal(s, ["NNNNN" + s[20:40]]))
assert fwd[0]["start"] == 20
assert fwd[0]["start"] + fwd[0]["length"] == 40
assert fwd[0]["top_strand_slice"] == (20, 40)
assert fwd[0]["anneal"] == s[20:40]
assert fwd[0]["overhang"] == "NNNNN"
assert fwd[0]["strand"] == 1
def check_primers(gfp, primerlist):
fwd, rev = anneal(gfp, primerlist, n_bases=16)
span_region_ok = []
for primer in fwd:
s = primer["start"]
l = len(primer["anneal"])
span_region_ok.append([s, l, -1, -1])
for primer in rev:
s = primer["start"]
l = len(primer["anneal"])
span_region_ok.append([-1, -1, s, l])
return span_region_ok
def test_anneal_end():
s = "ACGTGTATGTGATGATGTGCGTGTGTCGTGTAGCTTATTATATGCGGAGTCGTTGATGCTGTGAGT"
fwd, rev = anneal(s, [s[-16:]])
match = list(fwd)[0]
assert match["start"] == len(s) - 16
assert match["start"] + match["length"] == len(s)
def test_anneal_rev2(gfp):
fwd, rev = list(anneal(gfp, ["ANNNN" + reverse_complement(gfp[200:220])]))
assert rev
print(rev)
assert not fwd